The Human Rights Commission wants to be allowed to investigate allegations of human rights abuses involving MI5 or MI6 in Northern Ireland.
The Justice and Security Bill, currently before Parliament, exempts the intelligence services from being investigated by the commission.
Chief Commissioner Monica McWilliams said the bill dilutes her powers.
She said her office already deals with complaints from people who believe they are targets of covert surveillance.
"We shouldn't be stymied in our work ourselves, if we require documents," she told the BBC's Inside Politics programme.
"But you can imagine that stamp of national security, even where it is in the public interest or where there may be an issue of the incompatibility of human rights, we would ask that that not be stamped on our work and prevent us from doing the kind of work that we need to do."
"We say we should have the power to investigate matters retrospectively"
She said the current bill's exemption was "very wide-ranging".
"It would put a lot of limitations on what we would be able to investigate and we are hoping it could be amended," she said.
"It is in the public interest to investigate, whether it is agencies doing something incompatible with human rights.
"We say we should have the power to investigate matters retrospectively.
"We hope to have these powers by January 2008 so it would be a number of years after that before there would be evidence and documents available."
Established under the terms of the Good Friday Agreement, the commission's role is to ensure that human rights in Northern Ireland are protected in law, policy and practice.
MI5 is building a Northern Ireland centre near Holywood, County Down, and is due to take over responsibility for national security from the police.
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